TB-Profiler result

Run: ERR2229754

Summary

Run ID: ERR2229754

Sample name:

Date: 31-03-2023 17:32:47

Number of reads: 1089903

Percentage reads mapped: 99.18

Strain: lineage4.8;lineage4.4.1.1

Drug-resistance: Sensitive


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.85
lineage4.4.1 Euro-American (S-type) S;T None 0.06
lineage4.4.1.1 Euro-American S;Orphans None 0.06
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 0.19
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 762516 p.Gly904Cys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781409 c.-151T>G upstream_gene_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.95
rrl 1476091 n.2434T>C non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.17
PPE35 2167997 c.2616G>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 0.86
PPE35 2169281 c.1332T>G synonymous_variant 0.1
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169293 c.1320T>C synonymous_variant 0.16
PPE35 2169587 c.1026G>T synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 0.29
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222780 p.Asp129Tyr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.11
Rv3083 3448608 c.105G>A synonymous_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.12
aftB 4267104 p.Val578Glu missense_variant 0.12
aftB 4268839 c.-3C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408245 c.-43A>G upstream_gene_variant 0.11